When using project templates, two FGDB's are created. Steps to reproduce:
Create a project template that has, say, one connection to an ArcGIS Server, and one Folder Connection;
Save it to wherever, in this case, Portal;
Instruct another user to create a new project using this template;
Two "Databases" are present, the one that was present when you created the template and saved it(yellow), and a new one that is created when the user creates a new project using this template (red);
This is confusing, and asking end-users to "just delete the one you don't need" is unrealistic and extra work.